Evaluation of Structure Prediction and Molecular Docking Tools for Therapeutic Peptides in Clinical Use and Trials Targeting Coronary Artery Disease.

ABSTRACT: This study evaluates the performance of various structure prediction tools and molecular docking platforms for therapeutic peptides targeting coronary artery disease (CAD). Structure prediction tools, including AlphaFold 3, I-TASSER 5.1, and PEP-FOLD 4, were employed to generate accurate peptide conformations. These methods, ranging from deep-learning-based (AlphaFold) to template-based (I-TASSER 5.1) and fragment-based (PEP-FOLD), were selected for their proven capabilities in predicting reliable structures. Molecular docking was conducted using four platforms (HADDOCK 2.4, HPEPDOCK 2.0, ClusPro 2.0, and HawDock 2.0) to assess binding affinities and interactions. A 100 ns molecular dynamics (MD) simulation was performed to evaluate the stability of the peptide-receptor complexes, along wi

SUBMITTER: Alotaiq N 

PROVIDER: S-EPMC11765240 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature